Source code for cytoflow.views.kde_1d

#!/usr/bin/env python3.4
# coding: latin-1

# (c) Massachusetts Institute of Technology 2015-2018
# (c) Brian Teague 2018-2021
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <>.


from traits.api import provides, Constant
import matplotlib.pyplot as plt

import numpy as np
from sklearn.neighbors import KernelDensity
from statsmodels.nonparametric.bandwidths import bw_scott, bw_silverman

import cytoflow.utility as util

from .i_view import IView
from .base_views import Base1DView

[docs]@provides(IView) class Kde1DView(Base1DView): """ Plots a one-channel kernel density estimate, which is like a smoothed histogram. Attributes ---------- Examples -------- Make a little data set. .. plot:: :context: close-figs >>> import cytoflow as flow >>> import_op = flow.ImportOp() >>> import_op.tubes = [flow.Tube(file = "Plate01/RFP_Well_A3.fcs", ... conditions = {'Dox' : 10.0}), ... flow.Tube(file = "Plate01/CFP_Well_A4.fcs", ... conditions = {'Dox' : 1.0})] >>> import_op.conditions = {'Dox' : 'float'} >>> ex = import_op.apply() Plot a histogram .. plot:: :context: close-figs >>> flow.Kde1DView(channel = 'Y2-A', ... scale = 'log', ... huefacet = 'Dox').plot(ex) """ # traits id = Constant("") friendly_id = Constant("1D Kernel Density")
[docs] def plot(self, experiment, **kwargs): """ Plot a smoothed histogram view of a channel Parameters ---------- shade : bool If `True` (the default), shade the area under the plot. alpha : float, >=0 and <= 1 The transparency of the shading. 1 is opaque, 0 is transparent. Default = 0.25 kernel : str The kernel to use for the kernel density estimate. Choices are: - ``gaussian`` (the default) - ``tophat`` - ``epanechnikov`` - ``exponential`` - ``linear`` - ``cosine`` bw : str or float The bandwidth for the kernel, controls how lumpy or smooth the kernel estimate is. Choices are: - ``scott`` (the default) - ``1.059 * A * nobs ** (-1/5.)``, where ``A`` is ``min(std(X),IQR/1.34)`` - ``silverman`` - ``.9 * A * nobs ** (-1/5.)``, where ``A`` is ``min(std(X),IQR/1.34)`` If a float is given, it is the bandwidth. Note, this is in scaled units, not data units. gridsize : int (default = 100) How many times to compute the kernel? Notes ----- Other ``kwargs`` are passed to `matplotlib.pyplot.plot <>`_ """ if kwargs.get('orientation', 'vertical') == 'vertical': kwargs.setdefault('xlabel', kwargs.setdefault('ylabel', 'Density') else: # flip axis labels kwargs.setdefault('xlabel', 'Density') kwargs.setdefault('ylabel', super().plot(experiment, **kwargs)
def _grid_plot(self, experiment, grid, **kwargs): kwargs.setdefault('shade', True) kwargs.setdefault('orientation', "vertical") scale = kwargs.pop('scale')[] lim = kwargs.pop('lim')[],, scale = scale, **kwargs) ret = {} if kwargs['orientation'] == 'vertical': ret['xscale'] = scale ret['xlim'] = lim else: ret['yscale'] = scale ret['ylim'] = lim return ret
# yoinked from seaborn/, with modifications for scaling. def _univariate_kdeplot(data, scale=None, shade=False, kernel="gaussian", bw="scott", gridsize=100, cut=3, clip=None, legend=True, ax=None, orientation = "vertical", **kwargs): if ax is None: ax = plt.gca() if clip is None: clip = (-np.inf, np.inf) scaled_data = scale(data) # mask out the data that's not in the scale domain scaled_data = scaled_data[~np.isnan(scaled_data)] if kernel not in ['gaussian','tophat','epanechnikov','exponential','linear','cosine']: raise util.CytoflowOpError(None, "kernel must be one of ['gaussian'|'tophat'|'epanechnikov'|'exponential'|'linear'|'cosine']") if bw == 'scott': bw = bw_scott(scaled_data) elif bw == 'silverman': bw = bw_silverman(scaled_data) elif not isinstance(bw, float): raise util.CytoflowViewError(None, "Bandwith must be 'scott', 'silverman' or a float") support = _kde_support(scaled_data, bw, gridsize, cut, clip)[:, np.newaxis] kde = KernelDensity(kernel = kernel, bandwidth = bw).fit(scaled_data.to_numpy()[:, np.newaxis]) log_density = kde.score_samples(support) x = scale.inverse(support[:, 0]) y = np.exp(log_density) # Check if a label was specified in the call label = kwargs.pop("label", None) color = kwargs.pop("color", None) alpha = kwargs.pop("alpha", 0.25) # Draw the KDE plot and, optionally, shade if orientation == "vertical": ax.plot(x, y, color=color, label=label, **kwargs) if shade: ax.fill_between(x, 1e-12, y, facecolor=color, alpha=alpha) else: ax.plot(y, x, color=color, label=label, **kwargs) if shade: ax.fill_between(y, 1e-12, x, facecolor=color, alpha=alpha) return ax def _kde_support(data, bw, gridsize, cut, clip): """Establish support for a kernel density estimate.""" support_min = max(data.min() - bw * cut, clip[0]) support_max = min(data.max() + bw * cut, clip[1]) return np.linspace(support_min, support_max, gridsize) util.expand_class_attributes(Kde1DView) util.expand_method_parameters(Kde1DView, Kde1DView.plot)